I feel terrible that we had to throw the Emperors on the Moon table last year. It screwed with too much in my opinion.
Personally, I hate the idea (and power level) of the Emperor titan.
I promise that there will be a "no holds barred" table this year that is 100% completely open ended. This will be the only table that allows Emperors if I have things my way.
Sometime soon (hopefully within 2 weeks of this posting) Derek and I will open registration and have the "point restrictions" for the 5 tables.
The Megabattle is 2.5 months away... which is to say, "it's here."
My wargaming side agrees that Emperors are problematic. My modeling side thinks the Red Emperor was cool, and it would be a shame if he can't make another appearance. Alas, I suspect that the no holds barred table will have both war game focused players and model builders. Hopefully there will be both sorts on both sides of the table.
So long as the book rule about guns not firing below 45 degrees from horizontal is enforced, going up against an Emperor or other big titans might not be quite so bad. If one wants to tone down big titans some, don't allow every big weapon slot to fire a D template. An Emperor's six carapace weapons have generally turned into six d templates a turn. Might be a bit much.
Last year, excepting the four players who spent every point on big models (including the two emperors), I believe giving everyone else enough points for two baneblades worth of super-heavies would have covered everyone else's lists. My recommendation would be a no holds barred table, a couple of two baneblade tables, a one baneblade table, and a no super heavy table. The no holds barred table would have to be fairly flat for potential Emperors. The cavern table makes the most sense as a no superheavy table.
You might not want to lock which table will have how much superheavy until after the players start registering. When people register, along with asking a shirt size, ask how many points of super-heavies they intend to field, or how many points of super-heavies they would be comfortable fighting. If lots of folks want lots of super-heavies, you might adjust table limits to fit. If more folk want a more codex driven force, again, adjust to fit.